Atom **** in residue ASN 358 was not found in rtp entry ASN with 14 atoms while sorting atoms

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
Atom **** in residue ASN 358 was not found in rtp entry ASN with 14 atoms while sorting atoms.

I donot know why do I get such Fatal errors, I’m really confused and donot know how to solve such errors. I tried all my better way using gromacs documentations too.

2

Check in visualization software to see if the D138 residue in structure file miss atoms.
If hydrogen atoms are missing, you can use gmx pdb2gmx with -ignh option; if heavy atoms are missing, you need to fix the residue structure, such using SPDBV or PyMOL

3

Thank you, can you help me to fix the missing atom in PyMOL. OR atleast please give me the steps

4

Have you read Common errors when using GROMACS - GROMACS 2024.3 documentation? It might be enough to make sure that your atoms are correctly (according to the force field) named in the pdb file and/or make sure that you are using the correct terminal modification - if it is a terminal residue.

5

If indeed the side chain heavy atoms are missing (instead of due to the incorrect terminal residue as MagnusL said), the mutation funtion of PyMOL may helps you. In the top toolbar, Wizard → Mutagenesis → Protein, then choose the N358 residue and “mutate” it to a ASN residue, PyMOL would fix the side chain.